I like the idea of a project per module; I assume this requires you to use the complied module template. I have not had much luck witht he compiled modules, I guess I am too accustom to the traditionally web site structure and ways of editing them. With that said, I guess its time to defy the laws of tradition and switch to WAP's.
The reason I added a site to source control for each project was mainly workspace mapping issues. IE. I need to create a skin for project A and one for Project B. It was just easier to throw together a site add a skin using the template and go to work. I have not tried it, and would love input on, mapping your source control to a skin folder inside of your local DNN dev site. would this work? Is there a better option?